Multiple sequence alignment - TraesCS1A01G290400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G290400 chr1A 100.000 2507 0 0 1 2507 487009593 487012099 0.000000e+00 4630.0
1 TraesCS1A01G290400 chr1D 89.440 1392 78 23 606 1983 387215754 387217090 0.000000e+00 1692.0
2 TraesCS1A01G290400 chr1D 92.494 413 22 4 2104 2507 387217088 387217500 1.290000e-162 582.0
3 TraesCS1A01G290400 chr1B 90.728 1003 50 14 680 1647 520516719 520517713 0.000000e+00 1297.0
4 TraesCS1A01G290400 chr1B 91.727 411 26 4 2104 2507 520522044 520522453 4.680000e-157 564.0
5 TraesCS1A01G290400 chr1B 84.133 271 22 12 1715 1983 520521795 520522046 2.490000e-60 243.0
6 TraesCS1A01G290400 chr1B 91.803 61 4 1 1639 1698 520521691 520521751 1.600000e-12 84.2
7 TraesCS1A01G290400 chr7A 92.266 556 43 0 1 556 579092918 579093473 0.000000e+00 789.0
8 TraesCS1A01G290400 chr7A 89.434 530 56 0 1 530 731880067 731879538 0.000000e+00 669.0
9 TraesCS1A01G290400 chr4B 85.152 559 83 0 1 559 665977341 665976783 7.780000e-160 573.0
10 TraesCS1A01G290400 chr7B 84.201 557 88 0 3 559 556495588 556495032 2.190000e-150 542.0
11 TraesCS1A01G290400 chr7B 84.107 560 83 3 3 559 658420881 658420325 1.020000e-148 536.0
12 TraesCS1A01G290400 chr7B 85.586 111 12 4 1981 2088 442376265 442376156 2.040000e-21 113.0
13 TraesCS1A01G290400 chr4D 81.928 332 58 2 1 331 68800781 68800451 1.900000e-71 279.0
14 TraesCS1A01G290400 chr4D 85.321 109 8 5 1981 2088 108302774 108302673 3.410000e-19 106.0
15 TraesCS1A01G290400 chr6B 85.271 258 38 0 3 260 422340092 422340349 1.480000e-67 267.0
16 TraesCS1A01G290400 chr6B 91.176 102 9 0 446 547 422346463 422346564 3.360000e-29 139.0
17 TraesCS1A01G290400 chr6D 79.918 244 46 3 1033 1275 4182027 4181786 2.560000e-40 176.0
18 TraesCS1A01G290400 chr6D 92.857 84 4 1 1981 2064 193557200 193557119 1.220000e-23 121.0
19 TraesCS1A01G290400 chr2A 76.558 337 64 4 1082 1418 753045025 753044704 1.190000e-38 171.0
20 TraesCS1A01G290400 chr2A 73.046 371 83 7 1056 1425 752999303 752998949 5.670000e-22 115.0
21 TraesCS1A01G290400 chr2A 76.000 150 33 2 1189 1338 753041738 753041592 9.620000e-10 75.0
22 TraesCS1A01G290400 chr5A 90.000 130 7 3 1978 2106 219579229 219579353 2.000000e-36 163.0
23 TraesCS1A01G290400 chr2D 75.000 372 72 10 1056 1425 621140698 621140346 4.320000e-33 152.0
24 TraesCS1A01G290400 chr2D 82.353 119 9 2 1300 1418 621131667 621131561 2.660000e-15 93.5
25 TraesCS1A01G290400 chr2B 75.704 284 66 2 1056 1339 762065498 762065218 3.360000e-29 139.0
26 TraesCS1A01G290400 chrUn 75.352 284 67 2 1056 1339 307394494 307394774 1.560000e-27 134.0
27 TraesCS1A01G290400 chr7D 84.444 135 12 6 1977 2105 498292373 498292242 9.420000e-25 124.0
28 TraesCS1A01G290400 chr7D 92.941 85 4 2 1981 2065 74416592 74416674 3.390000e-24 122.0
29 TraesCS1A01G290400 chr7D 83.704 135 8 7 1981 2107 498292242 498292370 5.670000e-22 115.0
30 TraesCS1A01G290400 chr7D 92.063 63 4 1 2056 2118 118151640 118151701 1.240000e-13 87.9
31 TraesCS1A01G290400 chr5D 82.734 139 12 5 1974 2105 179264327 179264194 2.040000e-21 113.0
32 TraesCS1A01G290400 chr6A 81.679 131 15 6 1977 2106 73642653 73642775 1.590000e-17 100.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G290400 chr1A 487009593 487012099 2506 False 4630.00 4630 100.00000 1 2507 1 chr1A.!!$F1 2506
1 TraesCS1A01G290400 chr1D 387215754 387217500 1746 False 1137.00 1692 90.96700 606 2507 2 chr1D.!!$F1 1901
2 TraesCS1A01G290400 chr1B 520516719 520522453 5734 False 547.05 1297 89.59775 680 2507 4 chr1B.!!$F1 1827
3 TraesCS1A01G290400 chr7A 579092918 579093473 555 False 789.00 789 92.26600 1 556 1 chr7A.!!$F1 555
4 TraesCS1A01G290400 chr7A 731879538 731880067 529 True 669.00 669 89.43400 1 530 1 chr7A.!!$R1 529
5 TraesCS1A01G290400 chr4B 665976783 665977341 558 True 573.00 573 85.15200 1 559 1 chr4B.!!$R1 558
6 TraesCS1A01G290400 chr7B 556495032 556495588 556 True 542.00 542 84.20100 3 559 1 chr7B.!!$R2 556
7 TraesCS1A01G290400 chr7B 658420325 658420881 556 True 536.00 536 84.10700 3 559 1 chr7B.!!$R3 556

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
675 676 0.10741 TTTATAGTGGGCCAGGCACG 60.107 55.0 15.19 0.0 32.76 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 6141 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.0 0.0 0.0 0.0 4.12 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 6.072175 TGGCGTCTTTGATATAAGCAAAAACT 60.072 34.615 0.00 0.00 35.09 2.66
174 175 2.679639 GCGATTTCCCCACATACACAGA 60.680 50.000 0.00 0.00 0.00 3.41
189 190 1.556911 CACAGACAGCCCAAGGTATCT 59.443 52.381 0.00 0.00 0.00 1.98
316 317 1.938577 CATTGTCCAGAGCATTCCTCG 59.061 52.381 0.00 0.00 45.54 4.63
335 336 5.535406 TCCTCGTATAGGTCCAGAATTCTTC 59.465 44.000 4.86 0.00 46.62 2.87
354 355 1.627329 TCTGAGCTCACTGGCTTCATT 59.373 47.619 13.74 0.00 43.20 2.57
412 413 3.195825 CGAAGAAGAGGTGGGTGATAGTT 59.804 47.826 0.00 0.00 0.00 2.24
419 420 0.328258 GTGGGTGATAGTTGGTGCCT 59.672 55.000 0.00 0.00 0.00 4.75
556 557 1.815757 AGCCCCGGGTCAGTATAAAT 58.184 50.000 21.85 0.00 0.00 1.40
559 560 2.858745 CCCCGGGTCAGTATAAATTGG 58.141 52.381 21.85 0.00 0.00 3.16
560 561 2.488347 CCCCGGGTCAGTATAAATTGGG 60.488 54.545 21.85 0.00 0.00 4.12
561 562 2.440253 CCCGGGTCAGTATAAATTGGGA 59.560 50.000 14.18 0.00 36.17 4.37
562 563 3.073946 CCCGGGTCAGTATAAATTGGGAT 59.926 47.826 14.18 0.00 36.17 3.85
563 564 4.324267 CCGGGTCAGTATAAATTGGGATC 58.676 47.826 0.00 0.00 0.00 3.36
564 565 3.994392 CGGGTCAGTATAAATTGGGATCG 59.006 47.826 0.00 0.00 0.00 3.69
565 566 4.262292 CGGGTCAGTATAAATTGGGATCGA 60.262 45.833 0.00 0.00 0.00 3.59
566 567 5.617252 GGGTCAGTATAAATTGGGATCGAA 58.383 41.667 0.00 0.00 0.00 3.71
567 568 6.059484 GGGTCAGTATAAATTGGGATCGAAA 58.941 40.000 0.00 0.00 0.00 3.46
568 569 6.017357 GGGTCAGTATAAATTGGGATCGAAAC 60.017 42.308 0.00 0.00 0.00 2.78
569 570 6.766467 GGTCAGTATAAATTGGGATCGAAACT 59.234 38.462 0.00 0.00 0.00 2.66
570 571 7.282450 GGTCAGTATAAATTGGGATCGAAACTT 59.718 37.037 0.00 0.00 0.00 2.66
571 572 8.122952 GTCAGTATAAATTGGGATCGAAACTTG 58.877 37.037 0.00 0.00 0.00 3.16
572 573 7.282224 TCAGTATAAATTGGGATCGAAACTTGG 59.718 37.037 0.00 0.00 0.00 3.61
573 574 3.592898 AAATTGGGATCGAAACTTGGC 57.407 42.857 0.00 0.00 0.00 4.52
574 575 2.214376 ATTGGGATCGAAACTTGGCA 57.786 45.000 0.00 0.00 0.00 4.92
575 576 2.214376 TTGGGATCGAAACTTGGCAT 57.786 45.000 0.00 0.00 0.00 4.40
576 577 2.214376 TGGGATCGAAACTTGGCATT 57.786 45.000 0.00 0.00 0.00 3.56
577 578 2.524306 TGGGATCGAAACTTGGCATTT 58.476 42.857 0.00 0.00 0.00 2.32
578 579 3.691575 TGGGATCGAAACTTGGCATTTA 58.308 40.909 0.00 0.00 0.00 1.40
579 580 3.442273 TGGGATCGAAACTTGGCATTTAC 59.558 43.478 0.00 0.00 0.00 2.01
580 581 3.694566 GGGATCGAAACTTGGCATTTACT 59.305 43.478 0.00 0.00 0.00 2.24
581 582 4.157840 GGGATCGAAACTTGGCATTTACTT 59.842 41.667 0.00 0.00 0.00 2.24
582 583 5.095490 GGATCGAAACTTGGCATTTACTTG 58.905 41.667 0.00 0.00 0.00 3.16
583 584 4.497473 TCGAAACTTGGCATTTACTTGG 57.503 40.909 0.00 0.00 0.00 3.61
584 585 4.138290 TCGAAACTTGGCATTTACTTGGA 58.862 39.130 0.00 0.00 0.00 3.53
585 586 4.764823 TCGAAACTTGGCATTTACTTGGAT 59.235 37.500 0.00 0.00 0.00 3.41
586 587 5.242838 TCGAAACTTGGCATTTACTTGGATT 59.757 36.000 0.00 0.00 0.00 3.01
587 588 5.572896 CGAAACTTGGCATTTACTTGGATTC 59.427 40.000 0.00 0.00 0.00 2.52
588 589 4.701956 ACTTGGCATTTACTTGGATTCG 57.298 40.909 0.00 0.00 0.00 3.34
589 590 3.119495 ACTTGGCATTTACTTGGATTCGC 60.119 43.478 0.00 0.00 0.00 4.70
590 591 2.441410 TGGCATTTACTTGGATTCGCA 58.559 42.857 0.00 0.00 0.00 5.10
591 592 2.822561 TGGCATTTACTTGGATTCGCAA 59.177 40.909 0.00 0.00 0.00 4.85
592 593 3.446873 TGGCATTTACTTGGATTCGCAAT 59.553 39.130 0.00 0.00 0.00 3.56
593 594 4.081752 TGGCATTTACTTGGATTCGCAATT 60.082 37.500 0.00 0.00 0.00 2.32
594 595 4.869861 GGCATTTACTTGGATTCGCAATTT 59.130 37.500 0.00 0.00 0.00 1.82
595 596 6.039616 GGCATTTACTTGGATTCGCAATTTA 58.960 36.000 0.00 0.00 0.00 1.40
596 597 6.198966 GGCATTTACTTGGATTCGCAATTTAG 59.801 38.462 0.00 0.00 0.00 1.85
597 598 6.291796 GCATTTACTTGGATTCGCAATTTAGC 60.292 38.462 0.00 0.00 0.00 3.09
598 599 6.509418 TTTACTTGGATTCGCAATTTAGCT 57.491 33.333 0.00 0.00 0.00 3.32
599 600 4.622701 ACTTGGATTCGCAATTTAGCTC 57.377 40.909 0.00 0.00 0.00 4.09
600 601 3.063997 ACTTGGATTCGCAATTTAGCTCG 59.936 43.478 0.00 0.00 0.00 5.03
601 602 2.899976 TGGATTCGCAATTTAGCTCGA 58.100 42.857 0.00 0.00 0.00 4.04
602 603 2.607635 TGGATTCGCAATTTAGCTCGAC 59.392 45.455 0.00 0.00 0.00 4.20
603 604 2.032808 GGATTCGCAATTTAGCTCGACC 60.033 50.000 0.00 0.00 0.00 4.79
604 605 2.087501 TTCGCAATTTAGCTCGACCA 57.912 45.000 0.00 0.00 0.00 4.02
628 629 2.095853 GCAGCATGTGCGTACATACTTT 59.904 45.455 19.02 2.54 45.53 2.66
633 634 4.274069 CATGTGCGTACATACTTTCATGC 58.726 43.478 19.02 0.00 45.53 4.06
634 635 2.675844 TGTGCGTACATACTTTCATGCC 59.324 45.455 0.82 0.00 0.00 4.40
635 636 2.675844 GTGCGTACATACTTTCATGCCA 59.324 45.455 0.00 0.00 0.00 4.92
636 637 3.312421 GTGCGTACATACTTTCATGCCAT 59.688 43.478 0.00 0.00 0.00 4.40
637 638 4.509970 GTGCGTACATACTTTCATGCCATA 59.490 41.667 0.00 0.00 0.00 2.74
638 639 5.179368 GTGCGTACATACTTTCATGCCATAT 59.821 40.000 0.00 0.00 0.00 1.78
639 640 6.367695 GTGCGTACATACTTTCATGCCATATA 59.632 38.462 0.00 0.00 0.00 0.86
640 641 6.367695 TGCGTACATACTTTCATGCCATATAC 59.632 38.462 0.00 0.00 0.00 1.47
641 642 6.453791 GCGTACATACTTTCATGCCATATACG 60.454 42.308 0.00 0.00 32.98 3.06
642 643 6.034577 CGTACATACTTTCATGCCATATACGG 59.965 42.308 0.00 0.00 29.37 4.02
643 644 6.109156 ACATACTTTCATGCCATATACGGA 57.891 37.500 0.00 0.00 0.00 4.69
644 645 6.166279 ACATACTTTCATGCCATATACGGAG 58.834 40.000 0.00 0.00 0.00 4.63
671 672 7.231467 ACTATACAATTTTATAGTGGGCCAGG 58.769 38.462 19.02 0.00 41.68 4.45
672 673 3.031013 ACAATTTTATAGTGGGCCAGGC 58.969 45.455 6.40 1.26 0.00 4.85
673 674 3.030291 CAATTTTATAGTGGGCCAGGCA 58.970 45.455 15.19 0.00 0.00 4.75
674 675 2.137810 TTTTATAGTGGGCCAGGCAC 57.862 50.000 15.19 11.31 0.00 5.01
675 676 0.107410 TTTATAGTGGGCCAGGCACG 60.107 55.000 15.19 0.00 32.76 5.34
676 677 1.268992 TTATAGTGGGCCAGGCACGT 61.269 55.000 15.19 3.25 32.76 4.49
677 678 1.682451 TATAGTGGGCCAGGCACGTC 61.682 60.000 15.19 7.21 32.76 4.34
693 694 1.645455 GTCCGCACATGCATAGCAG 59.355 57.895 19.53 10.97 43.65 4.24
707 708 1.974249 TAGCAGAGACCGCGTACGTG 61.974 60.000 21.58 21.58 37.70 4.49
734 735 2.568623 AAGTTGATGGAAAGCGAGGT 57.431 45.000 0.00 0.00 0.00 3.85
737 738 2.301870 AGTTGATGGAAAGCGAGGTGTA 59.698 45.455 0.00 0.00 0.00 2.90
739 740 3.627395 TGATGGAAAGCGAGGTGTAAT 57.373 42.857 0.00 0.00 0.00 1.89
740 741 3.270027 TGATGGAAAGCGAGGTGTAATG 58.730 45.455 0.00 0.00 0.00 1.90
741 742 2.107950 TGGAAAGCGAGGTGTAATGG 57.892 50.000 0.00 0.00 0.00 3.16
747 757 0.108138 GCGAGGTGTAATGGTCAGCT 60.108 55.000 0.00 0.00 44.58 4.24
769 780 1.740025 GCCACAAGGTAGCATTGACTC 59.260 52.381 9.94 0.00 37.19 3.36
786 797 3.027029 GACTCGTTCAAAGTTCAAACGC 58.973 45.455 14.54 2.23 43.95 4.84
787 798 2.417239 ACTCGTTCAAAGTTCAAACGCA 59.583 40.909 14.54 6.39 43.95 5.24
840 851 4.785346 ATCATTCCAGCAGTCAACCTAT 57.215 40.909 0.00 0.00 0.00 2.57
890 911 2.161410 CGCTTGCTTTGCCTGTGTATAA 59.839 45.455 0.00 0.00 0.00 0.98
892 913 4.675146 CGCTTGCTTTGCCTGTGTATAAAT 60.675 41.667 0.00 0.00 0.00 1.40
893 914 4.563976 GCTTGCTTTGCCTGTGTATAAATG 59.436 41.667 0.00 0.00 0.00 2.32
895 916 4.339748 TGCTTTGCCTGTGTATAAATGGA 58.660 39.130 0.00 0.00 0.00 3.41
897 918 4.202050 GCTTTGCCTGTGTATAAATGGAGG 60.202 45.833 0.00 0.00 0.00 4.30
901 922 2.783510 CCTGTGTATAAATGGAGGGGGT 59.216 50.000 0.00 0.00 0.00 4.95
954 976 5.153675 AGCATCATCCATCTTCTCTCCTTA 58.846 41.667 0.00 0.00 0.00 2.69
957 979 3.319405 TCATCCATCTTCTCTCCTTACGC 59.681 47.826 0.00 0.00 0.00 4.42
967 996 3.799755 CCTTACGCCGCCTTGCAC 61.800 66.667 0.00 0.00 0.00 4.57
988 1017 0.536915 GCATTCCAGCCTCCATCTCC 60.537 60.000 0.00 0.00 0.00 3.71
1022 1051 1.933115 GCCGGCATGAAAACCATCGT 61.933 55.000 24.80 0.00 31.94 3.73
1119 1148 2.121832 TGGGACCTCACCACCGAT 59.878 61.111 0.00 0.00 31.83 4.18
1213 1242 3.898627 AACGTGCTCGAGGTCAGCG 62.899 63.158 15.58 12.48 40.01 5.18
1236 1265 0.520404 TCGACTACGACTCCTGCAAC 59.480 55.000 0.00 0.00 43.81 4.17
1293 1322 3.446570 ACCTACGTCGCCCTTCCG 61.447 66.667 0.00 0.00 0.00 4.30
1466 1503 0.036294 GCCGGGGCTACAATAGGATC 60.036 60.000 2.18 0.00 38.26 3.36
1539 1576 3.748083 TCTTCATTAGCTGATGATGCCC 58.252 45.455 20.62 0.00 36.05 5.36
1544 1581 2.665008 TAGCTGATGATGCCCGGTGC 62.665 60.000 0.00 4.04 41.77 5.01
1622 1659 0.249031 AAAAGTTGAGTTGCCGCAGC 60.249 50.000 0.00 0.00 40.48 5.25
1711 5735 1.975660 AGAGCGGGACTTCTAGCTAG 58.024 55.000 15.01 15.01 40.39 3.42
1712 5736 1.213430 AGAGCGGGACTTCTAGCTAGT 59.787 52.381 20.10 3.72 40.39 2.57
1713 5737 2.438763 AGAGCGGGACTTCTAGCTAGTA 59.561 50.000 20.10 10.24 40.39 1.82
1719 5770 3.243134 GGGACTTCTAGCTAGTACTTGCG 60.243 52.174 20.97 10.10 36.47 4.85
1723 5774 3.146618 TCTAGCTAGTACTTGCGTTGC 57.853 47.619 20.97 7.80 36.47 4.17
1726 5777 2.699954 AGCTAGTACTTGCGTTGCATT 58.300 42.857 20.97 1.86 38.76 3.56
1737 5788 2.032204 TGCGTTGCATTTTCAAATTGGC 60.032 40.909 0.00 0.00 31.71 4.52
1785 5836 3.674997 CTTGTGGCTTTCTACCTTGCTA 58.325 45.455 0.00 0.00 0.00 3.49
1804 5855 2.649831 AGCATTGCTTGTGGGTGAG 58.350 52.632 5.03 0.00 33.89 3.51
1822 5873 1.064208 GAGCAGCACAGCAGATCATTG 59.936 52.381 0.00 0.00 31.10 2.82
1833 5884 7.116662 GCACAGCAGATCATTGTTTAAATCAAA 59.883 33.333 0.00 0.00 0.00 2.69
1936 5989 8.102800 AGATGATAATTCGCAATAAAGCATGA 57.897 30.769 0.00 0.00 0.00 3.07
1937 5990 8.570488 AGATGATAATTCGCAATAAAGCATGAA 58.430 29.630 0.00 0.00 0.00 2.57
1980 6033 4.941263 TGCTACGTTTCCTCTAATGCATTT 59.059 37.500 18.75 1.81 0.00 2.32
1981 6034 6.110033 TGCTACGTTTCCTCTAATGCATTTA 58.890 36.000 18.75 5.63 0.00 1.40
1982 6035 6.036735 TGCTACGTTTCCTCTAATGCATTTAC 59.963 38.462 18.75 4.34 0.00 2.01
1983 6036 6.258068 GCTACGTTTCCTCTAATGCATTTACT 59.742 38.462 18.75 0.00 0.00 2.24
1984 6037 6.663944 ACGTTTCCTCTAATGCATTTACTC 57.336 37.500 18.75 0.48 0.00 2.59
1985 6038 5.585047 ACGTTTCCTCTAATGCATTTACTCC 59.415 40.000 18.75 0.00 0.00 3.85
1986 6039 5.007724 CGTTTCCTCTAATGCATTTACTCCC 59.992 44.000 18.75 0.00 0.00 4.30
1987 6040 5.975988 TTCCTCTAATGCATTTACTCCCT 57.024 39.130 18.75 0.00 0.00 4.20
1988 6041 5.552870 TCCTCTAATGCATTTACTCCCTC 57.447 43.478 18.75 0.00 0.00 4.30
1989 6042 4.348168 TCCTCTAATGCATTTACTCCCTCC 59.652 45.833 18.75 0.00 0.00 4.30
1990 6043 4.310769 CTCTAATGCATTTACTCCCTCCG 58.689 47.826 18.75 0.00 0.00 4.63
1991 6044 2.348411 AATGCATTTACTCCCTCCGG 57.652 50.000 5.99 0.00 0.00 5.14
1992 6045 0.179018 ATGCATTTACTCCCTCCGGC 60.179 55.000 0.00 0.00 0.00 6.13
1993 6046 1.526225 GCATTTACTCCCTCCGGCC 60.526 63.158 0.00 0.00 0.00 6.13
1994 6047 1.148498 CATTTACTCCCTCCGGCCC 59.852 63.158 0.00 0.00 0.00 5.80
1995 6048 1.307517 ATTTACTCCCTCCGGCCCA 60.308 57.895 0.00 0.00 0.00 5.36
1996 6049 0.917333 ATTTACTCCCTCCGGCCCAA 60.917 55.000 0.00 0.00 0.00 4.12
1997 6050 1.135068 TTTACTCCCTCCGGCCCAAA 61.135 55.000 0.00 0.00 0.00 3.28
1998 6051 1.135068 TTACTCCCTCCGGCCCAAAA 61.135 55.000 0.00 0.00 0.00 2.44
1999 6052 0.917333 TACTCCCTCCGGCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
2000 6053 0.917333 ACTCCCTCCGGCCCAAAATA 60.917 55.000 0.00 0.00 0.00 1.40
2001 6054 0.257616 CTCCCTCCGGCCCAAAATAA 59.742 55.000 0.00 0.00 0.00 1.40
2002 6055 0.257616 TCCCTCCGGCCCAAAATAAG 59.742 55.000 0.00 0.00 0.00 1.73
2003 6056 0.033503 CCCTCCGGCCCAAAATAAGT 60.034 55.000 0.00 0.00 0.00 2.24
2004 6057 1.102978 CCTCCGGCCCAAAATAAGTG 58.897 55.000 0.00 0.00 0.00 3.16
2005 6058 1.340600 CCTCCGGCCCAAAATAAGTGA 60.341 52.381 0.00 0.00 0.00 3.41
2006 6059 1.743394 CTCCGGCCCAAAATAAGTGAC 59.257 52.381 0.00 0.00 0.00 3.67
2007 6060 1.353022 TCCGGCCCAAAATAAGTGACT 59.647 47.619 0.00 0.00 0.00 3.41
2008 6061 1.743394 CCGGCCCAAAATAAGTGACTC 59.257 52.381 0.00 0.00 0.00 3.36
2009 6062 2.432444 CGGCCCAAAATAAGTGACTCA 58.568 47.619 0.00 0.00 0.00 3.41
2010 6063 2.817258 CGGCCCAAAATAAGTGACTCAA 59.183 45.455 0.00 0.00 0.00 3.02
2011 6064 3.365969 CGGCCCAAAATAAGTGACTCAAC 60.366 47.826 0.00 0.00 0.00 3.18
2012 6065 3.826729 GGCCCAAAATAAGTGACTCAACT 59.173 43.478 0.00 0.00 0.00 3.16
2013 6066 4.280929 GGCCCAAAATAAGTGACTCAACTT 59.719 41.667 0.00 0.00 42.89 2.66
2014 6067 5.221441 GGCCCAAAATAAGTGACTCAACTTT 60.221 40.000 0.00 0.00 40.77 2.66
2015 6068 5.691754 GCCCAAAATAAGTGACTCAACTTTG 59.308 40.000 0.00 0.00 40.77 2.77
2016 6069 6.682861 GCCCAAAATAAGTGACTCAACTTTGT 60.683 38.462 0.00 0.00 40.77 2.83
2017 6070 7.469456 GCCCAAAATAAGTGACTCAACTTTGTA 60.469 37.037 0.00 0.00 40.77 2.41
2018 6071 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2019 6072 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2023 6076 9.694137 AATAAGTGACTCAACTTTGTACTACTC 57.306 33.333 0.00 0.00 40.77 2.59
2024 6077 6.710597 AGTGACTCAACTTTGTACTACTCA 57.289 37.500 0.00 0.00 0.00 3.41
2025 6078 7.108841 AGTGACTCAACTTTGTACTACTCAA 57.891 36.000 0.00 0.00 0.00 3.02
2026 6079 6.979238 AGTGACTCAACTTTGTACTACTCAAC 59.021 38.462 0.00 0.00 0.00 3.18
2027 6080 6.979238 GTGACTCAACTTTGTACTACTCAACT 59.021 38.462 0.00 0.00 0.00 3.16
2028 6081 7.491696 GTGACTCAACTTTGTACTACTCAACTT 59.508 37.037 0.00 0.00 0.00 2.66
2029 6082 8.038944 TGACTCAACTTTGTACTACTCAACTTT 58.961 33.333 0.00 0.00 0.00 2.66
2030 6083 8.197988 ACTCAACTTTGTACTACTCAACTTTG 57.802 34.615 0.00 0.00 0.00 2.77
2031 6084 7.822822 ACTCAACTTTGTACTACTCAACTTTGT 59.177 33.333 0.00 0.00 0.00 2.83
2032 6085 9.309516 CTCAACTTTGTACTACTCAACTTTGTA 57.690 33.333 0.00 0.00 0.00 2.41
2033 6086 9.090692 TCAACTTTGTACTACTCAACTTTGTAC 57.909 33.333 0.00 0.00 35.43 2.90
2034 6087 9.095065 CAACTTTGTACTACTCAACTTTGTACT 57.905 33.333 0.00 0.00 35.76 2.73
2058 6111 9.174166 ACTAATTTTGTACAAAGTTGAGTCACT 57.826 29.630 29.11 11.00 33.31 3.41
2066 6119 9.781834 TGTACAAAGTTGAGTCACTTATTTTTG 57.218 29.630 0.00 1.16 35.87 2.44
2067 6120 9.783256 GTACAAAGTTGAGTCACTTATTTTTGT 57.217 29.630 13.18 13.18 35.87 2.83
2069 6122 9.783256 ACAAAGTTGAGTCACTTATTTTTGTAC 57.217 29.630 9.07 0.00 35.87 2.90
2070 6123 9.781834 CAAAGTTGAGTCACTTATTTTTGTACA 57.218 29.630 0.00 0.00 35.87 2.90
2074 6127 9.783256 GTTGAGTCACTTATTTTTGTACAAAGT 57.217 29.630 19.72 11.90 0.00 2.66
2076 6129 9.781834 TGAGTCACTTATTTTTGTACAAAGTTG 57.218 29.630 19.72 12.32 0.00 3.16
2077 6130 9.997482 GAGTCACTTATTTTTGTACAAAGTTGA 57.003 29.630 19.72 13.67 0.00 3.18
2079 6132 9.783256 GTCACTTATTTTTGTACAAAGTTGAGT 57.217 29.630 19.72 18.17 0.00 3.41
2080 6133 9.997482 TCACTTATTTTTGTACAAAGTTGAGTC 57.003 29.630 19.72 0.00 0.00 3.36
2081 6134 9.781834 CACTTATTTTTGTACAAAGTTGAGTCA 57.218 29.630 19.72 1.32 0.00 3.41
2082 6135 9.783256 ACTTATTTTTGTACAAAGTTGAGTCAC 57.217 29.630 19.72 0.00 0.00 3.67
2090 6143 9.781834 TTGTACAAAGTTGAGTCACTTATTTTG 57.218 29.630 5.64 8.80 35.87 2.44
2091 6144 8.402472 TGTACAAAGTTGAGTCACTTATTTTGG 58.598 33.333 12.94 0.78 35.87 3.28
2092 6145 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
2093 6146 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
2094 6147 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2095 6148 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
2096 6149 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
2097 6150 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
2098 6151 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
2099 6152 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2100 6153 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2101 6154 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2102 6155 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2153 6206 6.155049 ACAGCCATATAACTTGCCAATTTCTT 59.845 34.615 0.00 0.00 0.00 2.52
2154 6207 6.698766 CAGCCATATAACTTGCCAATTTCTTC 59.301 38.462 0.00 0.00 0.00 2.87
2202 6255 4.775780 AGGAACCTATACAACTACACAGCA 59.224 41.667 0.00 0.00 0.00 4.41
2215 6277 6.935741 ACTACACAGCAGTAATGAAACAAA 57.064 33.333 0.00 0.00 0.00 2.83
2375 6437 0.111061 TCTTGCAACTGTCCATGCCT 59.889 50.000 0.00 0.00 41.87 4.75
2379 6441 1.746615 CAACTGTCCATGCCTCCCG 60.747 63.158 0.00 0.00 0.00 5.14
2388 6450 1.349026 CCATGCCTCCCGTTCATATCT 59.651 52.381 0.00 0.00 0.00 1.98
2497 6559 5.293324 GGTTTTTGTGTTTCTCCATGTTTCC 59.707 40.000 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 1.287503 GGGGAAATCGCGCAAACAA 59.712 52.632 8.75 0.00 0.00 2.83
174 175 1.628846 ACGAAAGATACCTTGGGCTGT 59.371 47.619 0.00 0.00 31.91 4.40
335 336 2.008329 GAATGAAGCCAGTGAGCTCAG 58.992 52.381 18.89 6.90 44.11 3.35
354 355 4.471025 TCCTAATGATCAAAGCAGACAGGA 59.529 41.667 0.00 0.58 0.00 3.86
419 420 1.069090 GTGTCCGAGTGTGCCAAGA 59.931 57.895 0.00 0.00 0.00 3.02
556 557 2.214376 ATGCCAAGTTTCGATCCCAA 57.786 45.000 0.00 0.00 0.00 4.12
559 560 4.965119 AGTAAATGCCAAGTTTCGATCC 57.035 40.909 0.00 0.00 0.00 3.36
560 561 5.095490 CCAAGTAAATGCCAAGTTTCGATC 58.905 41.667 0.00 0.00 0.00 3.69
561 562 4.764823 TCCAAGTAAATGCCAAGTTTCGAT 59.235 37.500 0.00 0.00 0.00 3.59
562 563 4.138290 TCCAAGTAAATGCCAAGTTTCGA 58.862 39.130 0.00 0.00 0.00 3.71
563 564 4.497473 TCCAAGTAAATGCCAAGTTTCG 57.503 40.909 0.00 0.00 0.00 3.46
564 565 5.572896 CGAATCCAAGTAAATGCCAAGTTTC 59.427 40.000 0.00 0.00 0.00 2.78
565 566 5.469479 CGAATCCAAGTAAATGCCAAGTTT 58.531 37.500 0.00 0.00 0.00 2.66
566 567 4.618227 GCGAATCCAAGTAAATGCCAAGTT 60.618 41.667 0.00 0.00 0.00 2.66
567 568 3.119495 GCGAATCCAAGTAAATGCCAAGT 60.119 43.478 0.00 0.00 0.00 3.16
568 569 3.119531 TGCGAATCCAAGTAAATGCCAAG 60.120 43.478 0.00 0.00 0.00 3.61
569 570 2.822561 TGCGAATCCAAGTAAATGCCAA 59.177 40.909 0.00 0.00 0.00 4.52
570 571 2.441410 TGCGAATCCAAGTAAATGCCA 58.559 42.857 0.00 0.00 0.00 4.92
571 572 3.502191 TTGCGAATCCAAGTAAATGCC 57.498 42.857 0.00 0.00 0.00 4.40
572 573 6.291796 GCTAAATTGCGAATCCAAGTAAATGC 60.292 38.462 0.00 0.00 0.00 3.56
573 574 6.974622 AGCTAAATTGCGAATCCAAGTAAATG 59.025 34.615 0.00 0.00 38.13 2.32
574 575 7.100458 AGCTAAATTGCGAATCCAAGTAAAT 57.900 32.000 0.00 0.00 38.13 1.40
575 576 6.509418 AGCTAAATTGCGAATCCAAGTAAA 57.491 33.333 0.00 0.00 38.13 2.01
576 577 5.220586 CGAGCTAAATTGCGAATCCAAGTAA 60.221 40.000 0.00 0.00 38.13 2.24
577 578 4.270084 CGAGCTAAATTGCGAATCCAAGTA 59.730 41.667 0.00 0.00 38.13 2.24
578 579 3.063997 CGAGCTAAATTGCGAATCCAAGT 59.936 43.478 0.00 0.00 38.13 3.16
579 580 3.309682 TCGAGCTAAATTGCGAATCCAAG 59.690 43.478 0.00 0.00 38.13 3.61
580 581 3.063452 GTCGAGCTAAATTGCGAATCCAA 59.937 43.478 0.00 0.00 38.13 3.53
581 582 2.607635 GTCGAGCTAAATTGCGAATCCA 59.392 45.455 0.00 0.00 38.13 3.41
582 583 2.032808 GGTCGAGCTAAATTGCGAATCC 60.033 50.000 7.51 0.00 38.13 3.01
583 584 2.607635 TGGTCGAGCTAAATTGCGAATC 59.392 45.455 16.64 0.00 38.13 2.52
584 585 2.627945 TGGTCGAGCTAAATTGCGAAT 58.372 42.857 16.64 0.00 38.13 3.34
585 586 2.087501 TGGTCGAGCTAAATTGCGAA 57.912 45.000 16.64 0.00 38.13 4.70
586 587 1.933181 CATGGTCGAGCTAAATTGCGA 59.067 47.619 16.64 0.00 38.13 5.10
587 588 1.003545 CCATGGTCGAGCTAAATTGCG 60.004 52.381 16.64 0.00 38.13 4.85
588 589 1.268743 GCCATGGTCGAGCTAAATTGC 60.269 52.381 14.67 5.05 0.00 3.56
589 590 2.016318 TGCCATGGTCGAGCTAAATTG 58.984 47.619 14.67 5.77 0.00 2.32
590 591 2.292267 CTGCCATGGTCGAGCTAAATT 58.708 47.619 14.67 0.00 0.00 1.82
591 592 1.959042 CTGCCATGGTCGAGCTAAAT 58.041 50.000 14.67 0.00 0.00 1.40
592 593 0.744414 GCTGCCATGGTCGAGCTAAA 60.744 55.000 14.67 0.00 0.00 1.85
593 594 1.153369 GCTGCCATGGTCGAGCTAA 60.153 57.895 14.67 0.00 0.00 3.09
594 595 1.689243 ATGCTGCCATGGTCGAGCTA 61.689 55.000 24.25 15.41 32.41 3.32
595 596 3.040206 ATGCTGCCATGGTCGAGCT 62.040 57.895 24.25 12.91 32.41 4.09
596 597 2.515523 ATGCTGCCATGGTCGAGC 60.516 61.111 19.88 19.88 0.00 5.03
597 598 3.417601 CATGCTGCCATGGTCGAG 58.582 61.111 14.67 8.33 44.07 4.04
604 605 0.749091 ATGTACGCACATGCTGCCAT 60.749 50.000 0.00 8.71 43.89 4.40
628 629 7.114095 TGTATAGTACTCCGTATATGGCATGA 58.886 38.462 10.98 0.00 0.00 3.07
640 641 9.635520 CCCACTATAAAATTGTATAGTACTCCG 57.364 37.037 22.52 12.90 42.73 4.63
641 642 9.433153 GCCCACTATAAAATTGTATAGTACTCC 57.567 37.037 22.52 11.30 42.73 3.85
642 643 9.433153 GGCCCACTATAAAATTGTATAGTACTC 57.567 37.037 22.52 15.24 42.73 2.59
643 644 8.940982 TGGCCCACTATAAAATTGTATAGTACT 58.059 33.333 22.52 0.00 42.73 2.73
644 645 9.216117 CTGGCCCACTATAAAATTGTATAGTAC 57.784 37.037 22.52 16.17 42.73 2.73
645 646 8.380099 CCTGGCCCACTATAAAATTGTATAGTA 58.620 37.037 22.52 10.21 42.73 1.82
646 647 7.231467 CCTGGCCCACTATAAAATTGTATAGT 58.769 38.462 18.88 18.88 44.54 2.12
647 648 6.151144 GCCTGGCCCACTATAAAATTGTATAG 59.849 42.308 17.76 17.76 39.18 1.31
648 649 6.007703 GCCTGGCCCACTATAAAATTGTATA 58.992 40.000 7.66 0.00 0.00 1.47
649 650 4.832823 GCCTGGCCCACTATAAAATTGTAT 59.167 41.667 7.66 0.00 0.00 2.29
650 651 4.211920 GCCTGGCCCACTATAAAATTGTA 58.788 43.478 7.66 0.00 0.00 2.41
651 652 3.031013 GCCTGGCCCACTATAAAATTGT 58.969 45.455 7.66 0.00 0.00 2.71
652 653 3.030291 TGCCTGGCCCACTATAAAATTG 58.970 45.455 17.53 0.00 0.00 2.32
653 654 3.031013 GTGCCTGGCCCACTATAAAATT 58.969 45.455 17.53 0.00 0.00 1.82
654 655 2.666317 GTGCCTGGCCCACTATAAAAT 58.334 47.619 17.53 0.00 0.00 1.82
672 673 1.637934 CTATGCATGTGCGGACGTG 59.362 57.895 23.37 23.37 45.83 4.49
673 674 2.173669 GCTATGCATGTGCGGACGT 61.174 57.895 10.16 0.00 45.83 4.34
674 675 2.097661 CTGCTATGCATGTGCGGACG 62.098 60.000 22.82 8.94 45.83 4.79
675 676 0.811219 TCTGCTATGCATGTGCGGAC 60.811 55.000 24.66 0.00 45.83 4.79
676 677 0.531311 CTCTGCTATGCATGTGCGGA 60.531 55.000 25.86 25.86 45.83 5.54
677 678 0.531311 TCTCTGCTATGCATGTGCGG 60.531 55.000 21.83 21.83 45.83 5.69
678 679 0.580578 GTCTCTGCTATGCATGTGCG 59.419 55.000 10.16 9.99 45.83 5.34
693 694 2.202401 GTCCACGTACGCGGTCTC 60.202 66.667 20.98 9.94 43.45 3.36
707 708 2.194201 TTCCATCAACTTTCCCGTCC 57.806 50.000 0.00 0.00 0.00 4.79
734 735 0.322456 GTGGCCAGCTGACCATTACA 60.322 55.000 25.48 0.00 38.46 2.41
737 738 0.896940 CTTGTGGCCAGCTGACCATT 60.897 55.000 25.48 0.00 38.46 3.16
739 740 2.113774 CTTGTGGCCAGCTGACCA 59.886 61.111 18.93 18.93 0.00 4.02
740 741 2.124507 TACCTTGTGGCCAGCTGACC 62.125 60.000 17.39 15.06 36.63 4.02
741 742 0.674895 CTACCTTGTGGCCAGCTGAC 60.675 60.000 17.39 2.25 36.63 3.51
747 757 0.403655 TCAATGCTACCTTGTGGCCA 59.596 50.000 0.00 0.00 39.28 5.36
769 780 2.275253 GTGTGCGTTTGAACTTTGAACG 59.725 45.455 3.74 3.74 46.33 3.95
786 797 2.097954 CGGGGTTGAATGATCATGTGTG 59.902 50.000 9.46 0.00 34.96 3.82
787 798 2.026356 TCGGGGTTGAATGATCATGTGT 60.026 45.455 9.46 0.00 34.96 3.72
881 902 3.181443 GGACCCCCTCCATTTATACACAG 60.181 52.174 0.00 0.00 39.21 3.66
883 904 2.224450 CGGACCCCCTCCATTTATACAC 60.224 54.545 0.00 0.00 39.39 2.90
890 911 1.995626 CTGACGGACCCCCTCCATT 60.996 63.158 0.00 0.00 39.39 3.16
915 937 2.033602 CTTCACGGGGGTTGGGTC 59.966 66.667 0.00 0.00 0.00 4.46
957 979 2.180017 GAATGCAGTGCAAGGCGG 59.820 61.111 23.90 0.00 43.62 6.13
967 996 0.183014 AGATGGAGGCTGGAATGCAG 59.817 55.000 0.00 0.00 34.04 4.41
988 1017 2.658422 GGCCATGGGTTGCTGTTG 59.342 61.111 15.13 0.00 0.00 3.33
1007 1036 2.749621 AGGAGAACGATGGTTTTCATGC 59.250 45.455 12.19 0.00 38.62 4.06
1022 1051 0.173481 CGAGATCACGGCAAGGAGAA 59.827 55.000 4.47 0.00 0.00 2.87
1119 1148 4.752879 GACGCCCAGCTGCCGTAA 62.753 66.667 24.29 0.00 35.06 3.18
1217 1246 0.520404 GTTGCAGGAGTCGTAGTCGA 59.480 55.000 0.00 0.00 44.12 4.20
1450 1479 1.003696 GCCAGATCCTATTGTAGCCCC 59.996 57.143 0.00 0.00 0.00 5.80
1455 1484 3.069586 CGACAAGGCCAGATCCTATTGTA 59.930 47.826 5.01 0.00 34.82 2.41
1544 1581 5.862924 ACAGTCTTTACATCGGTTGAATG 57.137 39.130 0.00 0.00 0.00 2.67
1719 5770 3.251487 AGCAGCCAATTTGAAAATGCAAC 59.749 39.130 13.61 0.00 0.00 4.17
1723 5774 6.255020 GTGAGATAGCAGCCAATTTGAAAATG 59.745 38.462 0.00 0.00 0.00 2.32
1726 5777 4.158394 GGTGAGATAGCAGCCAATTTGAAA 59.842 41.667 0.00 0.00 0.00 2.69
1737 5788 2.672961 TTGGTTCGGTGAGATAGCAG 57.327 50.000 0.00 0.00 0.00 4.24
1804 5855 0.809385 ACAATGATCTGCTGTGCTGC 59.191 50.000 0.00 0.00 0.00 5.25
1833 5884 3.181478 GGTGCCAAGTTAGACGTATAGCT 60.181 47.826 0.26 0.26 0.00 3.32
1936 5989 3.598019 AATGGACAATCTGCGCATTTT 57.402 38.095 12.24 4.60 0.00 1.82
1937 5990 3.255725 CAAATGGACAATCTGCGCATTT 58.744 40.909 12.24 5.03 0.00 2.32
1986 6039 1.743394 GTCACTTATTTTGGGCCGGAG 59.257 52.381 5.05 0.00 0.00 4.63
1987 6040 1.353022 AGTCACTTATTTTGGGCCGGA 59.647 47.619 5.05 0.00 0.00 5.14
1988 6041 1.743394 GAGTCACTTATTTTGGGCCGG 59.257 52.381 0.00 0.00 0.00 6.13
1989 6042 2.432444 TGAGTCACTTATTTTGGGCCG 58.568 47.619 0.00 0.00 0.00 6.13
1990 6043 3.826729 AGTTGAGTCACTTATTTTGGGCC 59.173 43.478 0.00 0.00 0.00 5.80
1991 6044 5.453567 AAGTTGAGTCACTTATTTTGGGC 57.546 39.130 0.00 0.00 35.10 5.36
1992 6045 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
1993 6046 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
1997 6050 9.694137 GAGTAGTACAAAGTTGAGTCACTTATT 57.306 33.333 2.52 0.00 35.87 1.40
1998 6051 8.857098 TGAGTAGTACAAAGTTGAGTCACTTAT 58.143 33.333 2.52 0.00 35.87 1.73
1999 6052 8.229253 TGAGTAGTACAAAGTTGAGTCACTTA 57.771 34.615 2.52 0.00 35.87 2.24
2000 6053 7.108841 TGAGTAGTACAAAGTTGAGTCACTT 57.891 36.000 2.52 0.00 38.74 3.16
2001 6054 6.710597 TGAGTAGTACAAAGTTGAGTCACT 57.289 37.500 2.52 0.00 0.00 3.41
2002 6055 6.979238 AGTTGAGTAGTACAAAGTTGAGTCAC 59.021 38.462 2.52 0.00 0.00 3.67
2003 6056 7.108841 AGTTGAGTAGTACAAAGTTGAGTCA 57.891 36.000 2.52 0.00 0.00 3.41
2004 6057 8.328864 CAAAGTTGAGTAGTACAAAGTTGAGTC 58.671 37.037 2.52 0.00 31.15 3.36
2005 6058 7.822822 ACAAAGTTGAGTAGTACAAAGTTGAGT 59.177 33.333 2.52 6.12 32.54 3.41
2006 6059 8.197988 ACAAAGTTGAGTAGTACAAAGTTGAG 57.802 34.615 2.52 5.61 32.54 3.02
2007 6060 9.090692 GTACAAAGTTGAGTAGTACAAAGTTGA 57.909 33.333 2.52 0.00 36.11 3.18
2008 6061 9.095065 AGTACAAAGTTGAGTAGTACAAAGTTG 57.905 33.333 2.52 6.76 37.96 3.16
2032 6085 9.174166 AGTGACTCAACTTTGTACAAAATTAGT 57.826 29.630 20.89 19.19 0.00 2.24
2040 6093 9.781834 CAAAAATAAGTGACTCAACTTTGTACA 57.218 29.630 0.00 0.00 40.77 2.90
2041 6094 9.783256 ACAAAAATAAGTGACTCAACTTTGTAC 57.217 29.630 11.60 0.00 40.77 2.90
2043 6096 9.783256 GTACAAAAATAAGTGACTCAACTTTGT 57.217 29.630 15.36 15.36 40.77 2.83
2044 6097 9.781834 TGTACAAAAATAAGTGACTCAACTTTG 57.218 29.630 0.00 7.97 40.77 2.77
2048 6101 9.783256 ACTTTGTACAAAAATAAGTGACTCAAC 57.217 29.630 20.89 0.00 0.00 3.18
2050 6103 9.781834 CAACTTTGTACAAAAATAAGTGACTCA 57.218 29.630 20.89 0.00 0.00 3.41
2051 6104 9.997482 TCAACTTTGTACAAAAATAAGTGACTC 57.003 29.630 20.89 0.00 0.00 3.36
2053 6106 9.783256 ACTCAACTTTGTACAAAAATAAGTGAC 57.217 29.630 20.89 0.00 0.00 3.67
2054 6107 9.997482 GACTCAACTTTGTACAAAAATAAGTGA 57.003 29.630 20.89 15.17 0.00 3.41
2055 6108 9.781834 TGACTCAACTTTGTACAAAAATAAGTG 57.218 29.630 20.89 10.52 0.00 3.16
2056 6109 9.783256 GTGACTCAACTTTGTACAAAAATAAGT 57.217 29.630 20.89 19.47 0.00 2.24
2064 6117 9.781834 CAAAATAAGTGACTCAACTTTGTACAA 57.218 29.630 3.59 3.59 40.77 2.41
2065 6118 8.402472 CCAAAATAAGTGACTCAACTTTGTACA 58.598 33.333 0.00 0.00 40.77 2.90
2066 6119 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2067 6120 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2068 6121 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2069 6122 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2070 6123 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
2071 6124 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
2072 6125 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
2073 6126 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2074 6127 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2075 6128 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
2076 6129 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
2077 6130 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
2078 6131 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
2079 6132 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
2080 6133 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2081 6134 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2082 6135 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2083 6136 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2084 6137 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2085 6138 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2086 6139 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2087 6140 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2088 6141 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2089 6142 0.396695 GATGTACTCCCTCCGTCCCA 60.397 60.000 0.00 0.00 0.00 4.37
2090 6143 0.396695 TGATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
2091 6144 1.033574 CTGATGTACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
2092 6145 2.054232 TCTGATGTACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
2093 6146 2.379972 CTTCTGATGTACTCCCTCCGT 58.620 52.381 0.00 0.00 0.00 4.69
2094 6147 1.683917 CCTTCTGATGTACTCCCTCCG 59.316 57.143 0.00 0.00 0.00 4.63
2095 6148 2.432510 CACCTTCTGATGTACTCCCTCC 59.567 54.545 0.00 0.00 0.00 4.30
2096 6149 3.131400 GTCACCTTCTGATGTACTCCCTC 59.869 52.174 0.00 0.00 0.00 4.30
2097 6150 3.100671 GTCACCTTCTGATGTACTCCCT 58.899 50.000 0.00 0.00 0.00 4.20
2098 6151 2.832129 TGTCACCTTCTGATGTACTCCC 59.168 50.000 0.00 0.00 0.00 4.30
2099 6152 4.021016 AGTTGTCACCTTCTGATGTACTCC 60.021 45.833 0.00 0.00 0.00 3.85
2100 6153 5.140747 AGTTGTCACCTTCTGATGTACTC 57.859 43.478 0.00 0.00 0.00 2.59
2101 6154 6.665992 TTAGTTGTCACCTTCTGATGTACT 57.334 37.500 0.00 0.00 0.00 2.73
2102 6155 6.313905 CCATTAGTTGTCACCTTCTGATGTAC 59.686 42.308 0.00 0.00 0.00 2.90
2173 6226 8.192774 TGTGTAGTTGTATAGGTTCCTAATTCG 58.807 37.037 2.53 0.00 0.00 3.34
2215 6277 6.777580 TCTTTCTCTGCCATTTAGAGGTTTTT 59.222 34.615 0.00 0.00 41.54 1.94
2220 6282 7.050377 TGTATTCTTTCTCTGCCATTTAGAGG 58.950 38.462 0.00 0.00 41.54 3.69
2388 6450 9.739276 AAAGACAGAGTCCATATAATCACAAAA 57.261 29.630 0.00 0.00 32.18 2.44
2405 6467 1.068194 AGTCGCCGAAGAAAGACAGAG 60.068 52.381 0.00 0.00 36.18 3.35
2436 6498 5.070685 ACAGTAGAATCACCCAAAGGAAAC 58.929 41.667 0.00 0.00 36.73 2.78


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.